The 48-year-old has signed a three-year deal with the Silkmen after leaving Solihull Moors.
"I'm really pleased. It's happened really quickly but I'm joining a club with momentum and a club that are on the up," Yates told the club's official website.
"Everybody at the football club did a fantastic job last season and I just want to carry that on in a very competitive League Two.
"I'm looking forward to working with the players that are here but also bringing in some new faces too. I've been very impressed with the chairman and I'm sure we're going to work tirelessly to put together a squad that will do well next season."
Macclesfield are yet to announce who will make up Yates's backroom staff.